Revealing mistake: When Chunk opens the freezer in the Fratelli hideout to get the ice cream, if you look closely at the old dead man he moves his eyes several times between standing upright and falling over, and when he and Chunk are in the freezer together.
Continuity mistake: All the Goonies get soaked while in the Old Moss Garden wishing well, but when they are seen again in another part of the cave they are all dry, and there is not a sign of being soaked.
Continuity mistake: Right after Troy is humiliated at the wishing well, the movie cuts to a television food program, with Sloth's reflection visible in it. The problem is that Sloth's face is noticeably different in this reflection than the rest of the film. For instance, his left eye is only a bit lower than his right eye now, instead of it being considerably lower like it usually is.
Other mistake: In the bone organ scene, when Andy plays her first wrong note, you see Mouth in the next shot and he drops down before the floor even collapses.
Continuity mistake: When Mikey takes the skull necklace off Chester Copperpot, he accidentally pulls Chester's skull off his body. When Mikey does this, the skull is still touching the body, just detached and at the wrong angle. But the next shot we see with the skull, when Brand goes to place the skull back on the body, the skull is about a foot away from the body.
Other mistake: When Data puts his tape in the stereo he shuts the thing then the 007 music plays. He doesn't ever push play.
Continuity mistake: When Mr. Perkins delivers the papers to Brand at the house, the men are holding umbrellas. The umbrella handle on the left is facing outward, but after it cuts to Brand then back to the men, it is facing inward and then changes again after another angle change.
Continuity mistake: At the end when the father is about to sign the contract, and right about the part where Rosalita starts screaming in Spanish, the first page of the contract is folded up a little. In the very next shot, all the pages of the contract are flat.
Other mistake: When Data shoots a suction cup at Mrs. Fratelli's gun you can see Mouth in the background with his mouth open. Later Mrs. Fratelli pulls a ridiculous amount of jewels out of his now full mouth. DVD commentary offers an explanation to this, but it is still a mistake.
Revealing mistake: As the dead guy falls out the freezer, he is seen blinking.
Continuity mistake: At the Astoria Country Club, when the first shower handle disappears into the wall, the three surrounding tiles break off entirely from the wall. After the next few handles disappear, the wall with the first disappearing handle is shown, but now the square tiles are intact and only cracked.
Continuity mistake: Data jumps off the ship twice near the end. He starts his jump in one scene and jumps again in the following angle.
Revealing mistake: When Brand moves the rock and hundreds of bats fly, note that the blatant fake rock has a chunk of painting missing, revealing the white material underneath.
Other mistake: The Fratellis catch up with the Goonies near the waterfall. Francis shoots his gun upwards but the rocks that fall on him come from behind him.
Continuity mistake: While the Fratelli's carry the corpse bag, the hood on Mike's yellow raincoat changes positions between shots.
Continuity mistake: After removing the 'copper bone' necklace from Chester Copperpot, when Mikey puts the necklace around his neck, the cord's knot moves farther up between shots.
Continuity mistake: On Inferno's deck, when Data stubbornly takes a stand against the Fratellis, Mikey's and the others' facial expressions and positions repeatedly change between close-ups and wideshots.
Continuity mistake: When Troy sends the bucket down the well, in shots facing Andy and the rest, she stands behind the bucket, but in the shots facing Mikey as he tries to convince them all to continue on, Andy's left foot is atop the bucket, and so on.
Continuity mistake: On Inferno's deck, when Sloth jumps rope with Francis and Jake, in the close-up of his feet he wears all black high-tops with black laces, but in the previous and following shots he wears black high-tops with white soles and laces.
Revealing mistake: When the bats escape from the fireplace, it's obvious they are just black pieces of material.
Answer: According to Mikey and Mr. Walsh, one of his crewmen must have taken the map and fled when One Eyed Willie was murdering his crew. This is substantiated in the novelization.